Zenoni et al. - The potential of grapevine genomederived knowledge for present and future viticulture

Sara Zenoni, Anita Zamboni, Silvia Dal Santo, Marianna Fasoli, Mario Pezzotti e Giovanni Battista Tornielli*
Dipartimento di Biotecnologie, Università di Verona

nsegna_

Key words: genome, sequencing, transcriptome, gene expression, Vitis vinifera.

nsegna_

Abstract

nsegna_

In 2007 two high-quality drafts of the genome sequence of grapevine (Vitis vinifera) were published by two separate initiatives, the French- Italian public Consortium and the Italian-American collaboration. In the modern view, the genome is considered as the total content of the genetic material (DNA) of a cell of an organism, and it represents the potentiality of an organism. Grapevine is one of the world’s most important fruit crops, widely distributed and with a high economic impact. It also represents, through its products, the historical, social and traditional symbol of many geographical regions. By decoding the genome, new and advanced investigative tools are progressively being developed that, when used properly, will provide an enormous amount of basic, new, valuable and powerful information such as phylogeny, disease resistance, abiotic stresses, phenotypic plasticity, molecular breeding and system biology. Large-scale methods for the analysis of systems expression evolved from genomic sequencing by the Sanger method, and involved the census sequencing of cDNA libraries to generate collections of expressed sequence tags (ESTs) or short markers that were joined together in techniques such as serial analysis of gene expression (SAGE). For a period of about 10 years, sequence-based methods were largely replaced with microarrays, which allowed large numbers of transcripts to be quantified by hybridisation. In the last few years, the ultra-high-throughput potential of nextgeneration sequencing methods has allowed massive cDNA census sequencing technologies (collectively RNA-seq) to become more and more prevalent and, as the cost of sequencing continues to fall, it is likely to become the dominant approach once more. The development of high-throughput sequencing technologies enables the sequencing of total cDNA to derive an accurate measure of individual gene expression and differential splicing activity, and to discover novel regions of transcription, dramatically changing the way that the functional complexity of transcriptomes can be studied. The ability to analyse transcriptional changes in grapevine has yielded large amounts of data, beginning with the detection and quantification of single transcripts but now encompasses techniques that allow thousands of transcripts to be monitored simultaneously. Furthermore, the availability of the complete grapevine genome sequence allows for comprehensive transcriptomic experiments. Therefore, it is now much easier to identify candidate genes governing the key processes underlying organ development, particularly those relating to berry quality traits and stress responses. Such candidate genes represent a valuable pool of material for functional analyses, and particular research is still required to confirm genomic annotations and avoid annotation errors that would otherwise result in the misinterpretation of transcriptomic data. Altogether, these results constitute the basis for future studies and pay the way for the adoption of innovative methods to develop and support the Italian and worldwide viticulture of the XXI century. In this review we discuss the potential of technologies derived from knowledge of the genome such as the development of tools for the analysis of gene expression on a large scale, and some examples of their use in present and future viticulture.

nsegna_

 Download (members only)

Download full article

Zenoni.pdf